After playing the Song of Storms to drain the well, young Link can get an important item at the bottom of the well.
Equip the Hylian Shield. Otherwise, the Fire Keese in this area could burn up your Deku Shield.
Drain the Water
At the bottom of the well, crawl through the hole and climb down the ladder. Kill the skulltula, then walk through the wall next to the skeleton. It's an illusion!
In this area, go past the pool of water and follow the shallow water around the room in either direction. There is a Skulltula in the northwest corner, and a green bubble flying around in the area that flies counter-clockwise around the room. You can use your boomerang to stun it and use the slingshot to kill it. Eventually, after going around the shallow water around the room, you find a Triforce symbol on the floor near a stone mouth pouring out water. Play Zelda's Lullaby and all of the water will drain.
Return to the pool of water near where you entered this big room. Now that it is drained, you can hop into it or climb down on the vines on one side. Open the chest to get some bombs.
Reach the Mini-Boss
After opening the chest, crawl through the hole in the wall behind the chest. At the other end, kill the Skulltula, then climb up and go through the door.
Walk up to a hand to let it grab you. A scary monster appears. Wiggle the control stick and tap all of the buttons to escape the hand, then hit Dead Hand in the face with your sword until it turns around. Keep your distance from it, because it is about to go underground, and it will send out a shockwave that will hurt you. Then let a hand catch you again to make it reappear, and repeat the process until Dead Hand falls to the floor and starts twitching. This means that Dead Hand is finally really dead.
Get the Lens of Truth
A chest appears and Dead Hand fades away. Open the chest to get the Lens of Truth. When you use it, you can see the truth behind illusions like the fake wall next to the skeleton that you walked through to enter the dungeon. It can also reveal invisible monsters. But it costs magic to use it, so be sure to turn it off when you are not using it.
There is an invisible chest hidden behind the one that had the Lens of Truth in it. It contains a Gold Rupee, worth 200 rupees. Don't get it if you don't have room in your wallet.
Return to the main room.
Get a Key
After you climb out of the hole where the water used to be, look to the left into the passage where the water used to flow. Use the Lens of Truth to see a hole in the wall. Go through the fake wall to find a chest that contains a small key.
Get a Second Key
Leave the small room and turn left, then go straight along the drained path. When the path goes left, turn left and then stop. Use the Lens of Truth to see another hidden room here. Open the chest inside to get another small key.
Get the Compass
Leave this small room, then turn right, go straight, turn right at the corner, then stop. Use the Lens of Truth to find another fake wall. Go through it and use the Lens of Truth to look for the hole in the floor. Don't fall down the hole. Instead, open the chest to get the Compass.
Get a Third Key
Carefully leave the room where you got the Compass, then turn right, then go through the passage on the left. Climb down and open the chest to get a recovery heart. Climb up and go through the door.
Play Sun's Song to freeze the Gibdo and kill it. There are several caskets in this room. One of them, in the back of the room on the left, contains a key. You need to light the torch next to the casket to open it. (This means that if you use Din's Fire in this room, a bunch of monsters will come out of all of the caskets at once.) Use a Deku Stick to light the torch by the casket in the back on the left, then kill the Keese that come out and get the key from inside the casket.
Get a Gold Skulltula
Leave the room the way that you came in. Back in the central room, go straight ahead through the wall in front of you. Immediately turn left and go through the locked door there. You will find a Deku Baba inside, and the pots will fly at you. Kill the Gold Skulltula to get the token.
Get a Second Gold Skulltula
Leave the room. Keep your distance from the X made of wooden beams, because there is an invisible Skulltula and an invisible hole in the floor. You need to walk past the X and go through the other locked door in this room.Kill the Keese in the room, then use the Lens of Truth to see the invisible ledge around the edge of the room. Walk on the ledge to the far corner of the room and kill the Gold Skulltula, then leave the room.
Get a Third Gold Skulltula
Turn left and walk through the wall. Turn left, then turn on the Lens of Truth. There is an invisible hole in front of the scary portrait on the wall up ahead. Walk toward the portrait but don't fall in. Go to the right, then crawl through the hole to reach a locked door. Go through, and turn on the Lens of Truth to avoid falling into the holes in the floor. Kill the Keese, then throw a bomb at the Beamos to kill it (or just throw a Deku Nut to stun it). Open the chest to get five rupees, then go to the other side of the room. There is a Like Like on the other side of the door, so equip your slingshot, then go through.
Stay near the wall, then use the slingshot to kill the Like Like in this room. Then kill the gold skulltula. The chest here also contains 5 rupees.
Get the Map
The only thing left to collect in the dungeon is the map. If you don't want it, just leave the dungeon now.
If you do want the map, go to the previous room and fall down one of the holes. In this basement, follow the passage and bomb the boulders to get out. Go straight, then go to the left, between the two torches to the left of the poisonous pond. Bomb the boulders here, then kill the ReDead and get the map.
To leave this room, you could just use a warp song to get out, or you can collect the three silver rupees over the poisonous pond. After that, climb up the ladder to get the last two rupees. The bars will rise. Go through the door, then go through the wall in here to get to the main area once again. From there, you can leave the dungeon.
If you are ready, play the Prelude of Light to go back to the Temple of Time, or just go there on foot. You can't use the save-and-quit trick to return to the Temple of Time as child Link. In the Temple of Time, pull the Master Sword from its pedestal.
Next, play the Nocturne of Shadow to warp to Kakariko Graveyard, or if you haven't learned the song, go to Kakariko Village. There will be a cut scene if you have completed the Water Temple, and Sheik will teach you the Nocturne of Shadow.
After you play the Nocturne of Shadow, you will be looking down at the graveyard from a gate. Turn around and go down the stairs. Stand on the platform in the center, be sure to stand in the middle of it, and use Din's Fire. If you did it correctly, all of the torches will be lit and the door will slowly rise. Go through.